What exact reduce commands did you use?
On Fri, Apr 13, 2012 at 12:17 PM, Mahendra B Thapa <thapamb.mail.uc.edu>wrote:
> Dear Amber users
>
> Atom number of a pdb [ 2nd column ] is not continuous
> after using trim and reduce of AMBER command , instead " new" appears in
> the last column. May I have to use some programs ( like perl ) to get
> continuous as just before using the trim and reduce?
>
> *Before* using " trim and then reduce" command of AMBER ( a portion of PDB)
> ATOM 1 N MET A 0 2.087 8.287 -1.145 1.00
> 29.31 N
> ATOM 2 CA MET A 0 1.516 9.645 -0.899 1.00
> 28.06 C
> ATOM 3 C MET A 0 2.162 10.704 -1.788 1.00
> 27.19 C
> ATOM 4 O MET A 0 1.619 11.752 -2.238 1.00
> 26.90 O
> ATOM 5 CB MET A 0 1.819 9.901 0.601 1.00
> 31.06 C
> ATOM 6 N LYS A 1 3.440 10.436 -2.034 1.00
> 24.33 N
> ATOM 7 CA LYS A 1 4.326 11.276 -2.844 1.00
> 22.35 C
> ATOM 8 C LYS A 1 5.166 10.393 -3.771 1.00
> 20.85 C
> ATOM 9 O LYS A 1 5.580 9.289 -3.327 1.00
> 20.59 O
> ATOM 10 CB LYS A 1 5.252 12.085 -1.921 1.00
> 22.60 C
> ATOM 11 CG LYS A 1 4.400 13.116 -1.143 1.00
> 24.98 C
> ATOM 12 CD LYS A 1 5.237 13.720 -0.049 1.00
> 27.59 C
> ATOM 13 CE LYS A 1 4.283 14.413 0.937 1.00
> 29.67 C
> ATOM 14 NZ LYS A 1 3.765 15.649 0.280 1.00
> 30.63 N
>
>
>
> *After* using at first "trim" and then " reduce" command of AMBER ( a
> portion of PDB)
> ATOM 1 N MET A 0 2.087 8.287 -1.145 1.00
> 29.31 N
> ATOM 2 CA MET A 0 1.516 9.645 -0.899 1.00
> 28.06 C
> ATOM 3 C MET A 0 2.162 10.704 -1.788 1.00
> 27.19 C
> ATOM 4 O MET A 0 1.619 11.752 -2.238 1.00
> 26.90 O
> ATOM 5 CB MET A 0 1.819 9.901 0.601 1.00
> 31.06 C
> ATOM 0 H1 MET A 0 1.458 7.592 -0.796 1.00
> 29.31 H new
> ATOM 0 H2 MET A 0 2.220 8.154 -2.127 1.00
> 29.31 H new
> ATOM 0 H3 MET A 0 2.967 8.205 -0.676 1.00
> 29.31 H new
> ATOM 0 HA MET A 0 0.443 9.699 -1.134 1.00
> 28.06 H new
> ATOM 6 N LYS A 1 3.440 10.436 -2.034 1.00
> 24.33 N
> ATOM 7 CA LYS A 1 4.326 11.276 -2.844 1.00
> 22.35 C
>
> Thanks ,
> Mahendra Thapa
> University of Cincinnati
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 13 2012 - 15:30:03 PDT
